Hi all, I was wondering if it was possible for a user to specify the number of files to upload in Galaxy and have multiple file input boxes to upload updated on the wrapper page accordingly. A user will have from one to many files needed to be uploaded from a job. Right now I can see that galaxy does have the option for 1 file with the param "file". With an options tagset, I can have the user specify a range. The easiest solution I can think of right now is to have a 1-N option tag set and create 1-N file upload boxes corresponding to the option number. Is there a better way already built in to Galaxy to do this? Thanks!
Hi, I'm developing a barcode splitter, which will split barcodes of variable length and then put them into the history for downstream analysis (currently FASTX barcode splitter only splits barcodes of the same length and the user has to download the data through an html link). The number of output files can't be determined until the tool has executed as it will depend on the number of barcodes presented. Here is an abridged version of the tool xml file: <tool id="split_var_barcodes" name="Split barcodes of variable length" version="1.0.0" force_history_refresh="True"> <command interpreter="python">split_var_length_barcodes_wrapper.py $input $barcodes $output.extra_files_path $output </command> <inputs> <param format="txt" name="barcodes" type="data" label="Barcodes to use" /> <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> </inputs> <outputs> <data format="html" name="output" /> </outputs> </tool> When I run the tool, the $output file to which I write various tool progress stuff is written and is displayed in the history. Also, the spit barcode files are written to a sub-directory of the same name as the output file. In the Galaxy database, if the $output file is named dataset_11940.dat then an example barcode file name and path is: /home/galaxy/software/galaxy-central/database/files/011/dataset_11940_files /AACAGAGT.fastq Unfortunately, the split barcode files are not being displayed in the history, so I was wondering if anyone could see any problems in what I'm doing. Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
Hi Graham, I've created something similar myself. I've not put it on the toolshed yet, as I have to test it further, but it seems to work as expected. See code in attachment. Best regards, geert vandeweyer University of Antwerp On 12/05/2011 12:47 PM, graham etherington (TSL) wrote:
Hi, I'm developing a barcode splitter, which will split barcodes of variable length and then put them into the history for downstream analysis (currently FASTX barcode splitter only splits barcodes of the same length and the user has to download the data through an html link). The number of output files can't be determined until the tool has executed as it will depend on the number of barcodes presented. Here is an abridged version of the tool xml file:
<tool id="split_var_barcodes" name="Split barcodes of variable length" version="1.0.0" force_history_refresh="True"> <command interpreter="python">split_var_length_barcodes_wrapper.py $input $barcodes $output.extra_files_path $output</command> <inputs> <param format="txt" name="barcodes" type="data" label="Barcodes to use" /> <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> </inputs>
<outputs> <data format="html" name="output" /> </outputs> </tool>
When I run the tool, the $output file to which I write various tool progress stuff is written and is displayed in the history. Also, the spit barcode files are written to a sub-directory of the same name as the output file. In the Galaxy database, if the $output file is named dataset_11940.dat then an example barcode file name and path is: /home/galaxy/software/galaxy-central/database/files/011/dataset_11940_files /AACAGAGT.fastq
Unfortunately, the split barcode files are not being displayed in the history, so I was wondering if anyone could see any problems in what I'm doing.
Many thanks, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
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Graham, How are the output files being handled in split_var_length_barcodes_wrapper.py? See http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files for a reference-- you're going to want to follow the bottom example there involving $__new_file_path__ and the naming convention specified. On a side note, this is something I've brushed up against recently myself, I'd be very interested in seeing what you come up with. -Dannon On Dec 5, 2011, at 6:47 AM, graham etherington (TSL) wrote:
Hi, I'm developing a barcode splitter, which will split barcodes of variable length and then put them into the history for downstream analysis (currently FASTX barcode splitter only splits barcodes of the same length and the user has to download the data through an html link). The number of output files can't be determined until the tool has executed as it will depend on the number of barcodes presented. Here is an abridged version of the tool xml file:
<tool id="split_var_barcodes" name="Split barcodes of variable length" version="1.0.0" force_history_refresh="True"> <command interpreter="python">split_var_length_barcodes_wrapper.py $input $barcodes $output.extra_files_path $output </command> <inputs> <param format="txt" name="barcodes" type="data" label="Barcodes to use" /> <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> </inputs>
<outputs> <data format="html" name="output" /> </outputs> </tool>
When I run the tool, the $output file to which I write various tool progress stuff is written and is displayed in the history. Also, the spit barcode files are written to a sub-directory of the same name as the output file. In the Galaxy database, if the $output file is named dataset_11940.dat then an example barcode file name and path is: /home/galaxy/software/galaxy-central/database/files/011/dataset_11940_files /AACAGAGT.fastq
Unfortunately, the split barcode files are not being displayed in the history, so I was wondering if anyone could see any problems in what I'm doing.
Many thanks, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi, Thanks for the input. I've attached code (tool xml and perl script tool) and a test file for a simple example that creates variable amounts of files after tool execution. The test file is a simple 4 line text file for which new file is created for each line in it and then that line is written to the new file. An additional output file is also written with some runtime information in it. The files should run as-is, just edit your tool_conf.xml, upload Test.txt and it should work. This example creates the normal 'dataset_12345.dat' files and doesn't use a sub-directory (e.g. datset_12345_files). If someone can get that to work, that would be pretty good. All the best, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 05/12/2011 13:37, "Dannon Baker" <dannonbaker@me.com> wrote:
Graham,
How are the output files being handled in split_var_length_barcodes_wrapper.py? See http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files for a reference-- you're going to want to follow the bottom example there involving $__new_file_path__ and the naming convention specified.
On a side note, this is something I've brushed up against recently myself, I'd be very interested in seeing what you come up with.
-Dannon
On Dec 5, 2011, at 6:47 AM, graham etherington (TSL) wrote:
Hi, I'm developing a barcode splitter, which will split barcodes of variable length and then put them into the history for downstream analysis (currently FASTX barcode splitter only splits barcodes of the same length and the user has to download the data through an html link). The number of output files can't be determined until the tool has executed as it will depend on the number of barcodes presented. Here is an abridged version of the tool xml file:
<tool id="split_var_barcodes" name="Split barcodes of variable length" version="1.0.0" force_history_refresh="True"> <command interpreter="python">split_var_length_barcodes_wrapper.py $input $barcodes $output.extra_files_path $output </command> <inputs> <param format="txt" name="barcodes" type="data" label="Barcodes to use" /> <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> </inputs>
<outputs> <data format="html" name="output" /> </outputs> </tool>
When I run the tool, the $output file to which I write various tool progress stuff is written and is displayed in the history. Also, the spit barcode files are written to a sub-directory of the same name as the output file. In the Galaxy database, if the $output file is named dataset_11940.dat then an example barcode file name and path is:
/home/galaxy/software/galaxy-central/database/files/011/dataset_11940_fil es /AACAGAGT.fastq
Unfortunately, the split barcode files are not being displayed in the history, so I was wondering if anyone could see any problems in what I'm doing.
Many thanks, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Graham, There was an issue with the dataset collection code that was preventing this sample wrapper from working. This has been fixed in 6426:187267753315, and the wrapper now functions properly for me, displaying all 5 files. Let me know if this works for you after you've updated. Thanks! -Dannon On Dec 6, 2011, at 7:02 AM, graham etherington (TSL) wrote:
Hi, Thanks for the input. I've attached code (tool xml and perl script tool) and a test file for a simple example that creates variable amounts of files after tool execution. The test file is a simple 4 line text file for which new file is created for each line in it and then that line is written to the new file. An additional output file is also written with some runtime information in it. The files should run as-is, just edit your tool_conf.xml, upload Test.txt and it should work. This example creates the normal 'dataset_12345.dat' files and doesn't use a sub-directory (e.g. datset_12345_files). If someone can get that to work, that would be pretty good. All the best, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
On 05/12/2011 13:37, "Dannon Baker" <dannonbaker@me.com> wrote:
Graham,
How are the output files being handled in split_var_length_barcodes_wrapper.py? See http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files for a reference-- you're going to want to follow the bottom example there involving $__new_file_path__ and the naming convention specified.
On a side note, this is something I've brushed up against recently myself, I'd be very interested in seeing what you come up with.
-Dannon
On Dec 5, 2011, at 6:47 AM, graham etherington (TSL) wrote:
Hi, I'm developing a barcode splitter, which will split barcodes of variable length and then put them into the history for downstream analysis (currently FASTX barcode splitter only splits barcodes of the same length and the user has to download the data through an html link). The number of output files can't be determined until the tool has executed as it will depend on the number of barcodes presented. Here is an abridged version of the tool xml file:
<tool id="split_var_barcodes" name="Split barcodes of variable length" version="1.0.0" force_history_refresh="True"> <command interpreter="python">split_var_length_barcodes_wrapper.py $input $barcodes $output.extra_files_path $output </command> <inputs> <param format="txt" name="barcodes" type="data" label="Barcodes to use" /> <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> </inputs>
<outputs> <data format="html" name="output" /> </outputs> </tool>
When I run the tool, the $output file to which I write various tool progress stuff is written and is displayed in the history. Also, the spit barcode files are written to a sub-directory of the same name as the output file. In the Galaxy database, if the $output file is named dataset_11940.dat then an example barcode file name and path is:
/home/galaxy/software/galaxy-central/database/files/011/dataset_11940_fil es /AACAGAGT.fastq
Unfortunately, the split barcode files are not being displayed in the history, so I was wondering if anyone could see any problems in what I'm doing.
Many thanks, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
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<multi.pl><multi.xml><Test.txt>
participants (4)
-
Dannon Baker -
Geert Werk -
graham etherington (TSL) -
Roger Ngo